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Chakraborty A, Samant D, Sarkar R, Sangeet S, Prusty S, Roy S. RNA's Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events. J Phys Chem Lett 2024; 15:6115-6125. [PMID: 38830201 DOI: 10.1021/acs.jpclett.4c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
In the TAR RNA of immunodeficiency viruses, an allosteric communication exists between a distant loop and a bulge. The bulge interacts with the TAT protein vital for transactivating viral RNA, while the loop interacts with cyclin-T1, contingent on TAT binding. Through extensive atomistic and free energy simulations, we investigate TAR-TAT binding in nonpathogenic bovine immunodeficiency virus (BIV) and pathogenic human immunodeficiency virus (HIV). Thermodynamic analysis reveals enthalpically driven binding in BIV and entropically favored binding in HIV. The broader global basin in HIV is attributed to binding-induced loop fluctuation, corroborated by nuclear magnetic resonance (NMR), indicating classical entropic allostery onset. While this loop fluctuation affects the TAT binding affinity, it generates a binding-competent conformation that aids subsequent effector (cyclin-T1) binding. This study underscores how two structurally similar apo-RNA scaffolds adopt distinct conformational selection mechanisms to drive enthalpic and entropic allostery, influencing protein affinity in the signaling cascade.
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Affiliation(s)
- Amrita Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Dibyamanjaree Samant
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Satyam Sangeet
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Sangram Prusty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
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2
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Fanara S, Schloesser M, Joris M, De Franco S, Vandevenne M, Kerff F, Hanikenne M, Motte P. The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2280-2298. [PMID: 38180875 DOI: 10.1093/jxb/erae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each SR45 domains by examining their involvement in: (i) the spatial distribution of SR45; (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components; and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RRM domain specifically binds purine-rich RNA motifs via three residues (H101, H141, and Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues probably phosphorylated by kinases from both the CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.
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Affiliation(s)
- Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marine Joris
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Simona De Franco
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Marylène Vandevenne
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- InBioS-Center for Protein Engineering, Laboratory of Crystallography, University of Liège, 4000, Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, 4000, Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
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3
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Lewinski M, Steffen A, Kachariya N, Elgner M, Schmal C, Messini N, Köster T, Reichel M, Sattler M, Zarnack K, Staiger D. Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:203-224. [PMID: 38124335 DOI: 10.1111/tpj.16601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The importance of RNA-binding proteins (RBPs) for plant responses to environmental stimuli and development is well documented. Insights into the portfolio of RNAs they recognize, however, clearly lack behind the understanding gathered in non-plant model organisms. Here, we characterize binding of the circadian clock-regulated Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 7 (AtGRP7) to its target transcripts. We identified novel RNA targets from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) data using an improved bioinformatics pipeline that will be broadly applicable to plant RBP iCLIP data. 2705 transcripts with binding sites were identified in plants expressing AtGRP7-GFP that were not recovered in plants expressing an RNA-binding dead variant or GFP alone. A conserved RNA motif enriched in uridine residues was identified at the AtGRP7 binding sites. NMR titrations confirmed the preference of AtGRP7 for RNAs with a central U-rich motif. Among the bound RNAs, circadian clock-regulated transcripts were overrepresented. Peak abundance of the LHCB1.1 transcript encoding a chlorophyll-binding protein was reduced in plants overexpressing AtGRP7 whereas it was elevated in atgrp7 mutants, indicating that LHCB1.1 was regulated by AtGRP7 in a dose-dependent manner. In plants overexpressing AtGRP7, the LHCB1.1 half-life was shorter compared to wild-type plants whereas in atgrp7 mutant plants, the half-life was significantly longer. Thus, AtGRP7 modulates circadian oscillations of its in vivo binding target LHCB1.1 by affecting RNA stability.
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Alexander Steffen
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Mareike Elgner
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Niki Messini
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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4
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Roca-Martínez J, Kang HS, Sattler M, Vranken W. Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models. NAR Genom Bioinform 2024; 6:lqae002. [PMID: 38288375 PMCID: PMC10823583 DOI: 10.1093/nargab/lqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
The RNA recognition motif (RRM) is the most prevalent RNA binding domain in eukaryotes and is involved in most RNA metabolism processes. Single RRM domains have a limited RNA specificity and affinity and tend to be accompanied by other RNA binding domains, frequently additional RRMs that contribute to an avidity effect. Within multi-RRM proteins, the most common arrangement are tandem RRMs, with two domains connected by a variable linker. Despite their prevalence, little is known about the features that lead to specific arrangements, and especially the role of the connecting linker. In this work, we present a novel and robust way to investigate the relative domain orientation in multi-domain proteins using inter-domain vectors referenced to a stable secondary structure element. We apply this method to tandem RRM domains and cluster experimental tandem RRM structures according to their inter-domain and linker-domain contacts, and report how this correlates with their orientation. By extending our analysis to AlphaFold2 predicted structures, with particular attention to the inter-domain predicted aligned error, we identify new orientations not reported experimentally. Our analysis provides novel insights across a range of tandem RRM orientations that may help for the design of proteins with a specific RNA binding mode.
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Affiliation(s)
- Joel Roca-Martínez
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Hyun-Seo Kang
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, 85764 Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, 85747 Garching, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, 85764 Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, 85747 Garching, Germany
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
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5
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Kara H, Axer A, Muskett FW, Bueno-Alejo CJ, Paschalis V, Taladriz-Sender A, Tubasum S, Vega MS, Zhao Z, Clark AW, Hudson AJ, Eperon IC, Burley GA, Dominguez C. 2'- 19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Front Mol Biosci 2024; 11:1325041. [PMID: 38419689 PMCID: PMC10899400 DOI: 10.3389/fmolb.2024.1325041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.
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Affiliation(s)
- Hesna Kara
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Alexander Axer
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Frederick W Muskett
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Carlos J Bueno-Alejo
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Vasileios Paschalis
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Sumera Tubasum
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Marina Santana Vega
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Zhengyun Zhao
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Alasdair W Clark
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J Hudson
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Ian C Eperon
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Glenn A Burley
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Cyril Dominguez
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
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6
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Okutman O, Gürbüz AS, Büyük U, Real E, Leconte R, Chennen K, Mayer C, Muller J, Le May N, Viville S. Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage. J Assist Reprod Genet 2024; 41:311-322. [PMID: 38177974 PMCID: PMC10894787 DOI: 10.1007/s10815-023-03009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Women undergoing controlled ovarian hyperstimulation prior to in vitro fertilization (IVF) are treated using various protocols to induce multiple follicular growths. Complete failure of all oocytes to mature during IVF cycles is rare; however, it is a known cause of primary female infertility. Recently, pathogenic variations in a few genes have been identified in women with oocyte maturation defects; however, the underlying genetic causes remain largely unknown.This study included a Turkish family comprising three sisters with recurring oocyte maturation arrest at the germinal vesicle stage after multiple ovarian stimulations. Exome sequencing revealed a homozygous missense variant (c.1037C>T, p.Ala346Val) in the EPAB gene (also known as PABPC1L) in all three affected sisters, which was either absent or heterozygous in the unaffected family members. Functional experiments confirming the pathogenicity of the variant were performed by transfecting HEK293T cells and demonstrated the instability and increased rate of proteolysis of the mutated PABPC1L/EPAB protein. The identified variant, located in the well-conserved fourth RNA recognition motif (RRM4), in silico 3D modelling suggested changes in the physical properties of the pathogenic variant of PABPC1L/EPAB. Our findings validate PABPC1L/EPAB as an essential genetic contributor to the oocyte maturation process in humans and have direct implications for the genetic counselling of patients and their family members.
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Affiliation(s)
- O Okutman
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Hôpital Erasme, Service de Gynécologie-Obstetrique, Clinique de Fertilité, Route de Lennik, 808, 1070, Brussels, Belgium
| | | | - U Büyük
- Department of Molecular Biology and Genetics, Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey
| | - E Real
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - R Leconte
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - K Chennen
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
| | - C Mayer
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
- UFR Sciences de La Vie, Université Paris Cité, 75013, Paris, France
| | - J Muller
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée Au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - N Le May
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - S Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France.
- Laboratoire de Diagnostic Génétique, Unité de Génétique de L'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France.
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7
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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8
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Kairouani A, Pontier D, Picart C, Mounet F, Martinez Y, Le-Bot L, Fanuel M, Hammann P, Belmudes L, Merret R, Azevedo J, Carpentier MC, Gagliardi D, Couté Y, Sibout R, Bies-Etheve N, Lagrange T. Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis. eLife 2023; 12:RP88207. [PMID: 37773033 PMCID: PMC10541177 DOI: 10.7554/elife.88207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
Deciphering the mechanism of secondary cell wall/SCW formation in plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although transcriptional regulation is essential for SCW formation, little is known about the implication of post-transcriptional mechanisms in this process. Here we report that two bonafide RNA-binding proteins homologous to the animal translational regulator Musashi, MSIL2 and MSIL4, function redundantly to control SCW formation in Arabidopsis. MSIL2/4 interactomes are similar and enriched in proteins involved in mRNA binding and translational regulation. MSIL2/4 mutations alter SCW formation in the fibers, leading to a reduction in lignin deposition, and an increase of 4-O-glucuronoxylan methylation. In accordance, quantitative proteomics of stems reveal an overaccumulation of glucuronoxylan biosynthetic machinery, including GXM3, in the msil2/4 mutant stem. We showed that MSIL4 immunoprecipitates GXM mRNAs, suggesting a novel aspect of SCW regulation, linking post-transcriptional control to the regulation of SCW biosynthesis genes.
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Affiliation(s)
- Alicia Kairouani
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, INP, UMR5546Castanet-TolosanFrance
| | - Yves Martinez
- FRAIB-CNRS Plateforme ImagerieCastanet-TolosanFrance
| | - Lucie Le-Bot
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Mathieu Fanuel
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
- PROBE research infrastructure, BIBS Facility, INRAENantesFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade de CNRS, Université de StrasbourgStrasbourgFrance
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Remy Merret
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Jacinthe Azevedo
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, IBMP, CNRS, Université de StrasbourgStrasbourgFrance
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Richard Sibout
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
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9
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Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M. Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Nat Commun 2023; 14:4233. [PMID: 37454201 PMCID: PMC10349855 DOI: 10.1038/s41467-023-39961-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains to cis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.
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Affiliation(s)
- Komal Soni
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sophie Bonnal
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Arie Geerlof
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Ralf Stehle
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany.
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10
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Gaurav AK, Afrin M, Yang X, Saha A, Sayeed SKA, Pan X, Ji Z, Wong KB, Zhang M, Zhao Y, Li B. The RRM-mediated RNA binding activity in T. brucei RAP1 is essential for VSG monoallelic expression. Nat Commun 2023; 14:1576. [PMID: 36949076 PMCID: PMC10033678 DOI: 10.1038/s41467-023-37307-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Trypanosoma brucei is a protozoan parasite that causes human African trypanosomiasis. Its major surface antigen VSG is expressed from subtelomeric loci in a strictly monoallelic manner. We previously showed that the telomere protein TbRAP1 binds dsDNA through its 737RKRRR741 patch to silence VSGs globally. How TbRAP1 permits expression of the single active VSG is unknown. Through NMR structural analysis, we unexpectedly identify an RNA Recognition Motif (RRM) in TbRAP1, which is unprecedented for RAP1 homologs. Assisted by the 737RKRRR741 patch, TbRAP1 RRM recognizes consensus sequences of VSG 3'UTRs in vitro and binds the active VSG RNA in vivo. Mutating conserved RRM residues abolishes the RNA binding activity, significantly decreases the active VSG RNA level, and derepresses silent VSGs. The competition between TbRAP1's RNA and dsDNA binding activities suggests a VSG monoallelic expression mechanism in which the active VSG's abundant RNA antagonizes TbRAP1's silencing effect, thereby sustaining its full-level expression.
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Grants
- R01 AI066095 NIAID NIH HHS
- S10 OD025252 NIH HHS
- Research Grants Council grants PolyU 151062/18M, 15103819, 15106421, R5050-18 and AoE/M-09/12, Shenzhen Basic Research Program of China (JCYJ20170818104619974, JCYJ20210324133803009) (PI, Zhao).
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
- U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)
- Research Grants Council, University Grants Committee (RGC, UGC)
- Research Grants Council grants PolyU 151062/18M, 15103819, 15106421, R5050-18 and AoE/M-09/12 (Zhao), Shenzhen Basic Research Programs of China JCYJ20170818104619974 & JCYJ20210324133803009 (Zhao). Shenzhen Basic Research Program of China JCYJ20220818100215033 (Zhang). Research Grants Council grant C4041-18E (Wong, Zhang, Zhao).
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Affiliation(s)
- Amit Kumar Gaurav
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Marjia Afrin
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
- Institute for Stem cell Biology and Regenerative Medicine, Stanford School of medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Xian Yang
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, People's Republic of China
| | - Arpita Saha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, 28029, Spain
| | - S K Abdus Sayeed
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
| | - Xuehua Pan
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, People's Republic of China
| | - Zeyang Ji
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong (CUHK), Shatin, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China.
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, People's Republic of China.
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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11
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Xu J, Liu X, Wu S, Zhang D, Liu X, Xia P, Ling J, Zheng K, Xu M, Shen Y, Zhang J, Yu P. RNA-binding proteins in metabolic-associated fatty liver disease (MAFLD): From mechanism to therapy. Biosci Trends 2023; 17:21-37. [PMID: 36682800 DOI: 10.5582/bst.2022.01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease globally and seriously increases the public health burden, affecting approximately one quarter of the world population. Recently, RNA binding proteins (RBPs)-related pathogenesis of MAFLD has received increasing attention. RBPs, vividly called the gate keepers of MAFLD, play an important role in the development of MAFLD through transcription regulation, alternative splicing, alternative polyadenylation, stability and subcellular localization. In this review, we describe the mechanisms of different RBPs in the occurrence and development of MAFLD, as well as list some drugs that can improve MAFLD by targeting RBPs. Considering the important role of RBPs in the development of MAFLD, elucidating the RNA regulatory networks involved in RBPs will facilitate the design of new drugs and biomarkers discovery.
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Affiliation(s)
- Jiawei Xu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyu Liu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shuqin Wu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Liu
- Department of Cardiology, The Second Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kai Zheng
- Medical Care Strategic Customer Department, China Merchants Bank Shenzhen Branch, Shenzhen, Guangdong, Guangdong, China
| | - Minxuan Xu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yunfeng Shen
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jing Zhang
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Yu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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12
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Chen X, Wang Y, Xu Z, Cheng ML, Ma QQ, Li RT, Wang ZJ, Zhao H, Zuo X, Li XF, Fang X, Qin CF. Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1. Nat Commun 2023; 14:1134. [PMID: 36854751 PMCID: PMC9972320 DOI: 10.1038/s41467-023-36838-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Human RNA binding protein Musashi-1 (MSI1) plays a critical role in neural progenitor cells (NPCs) by binding to various host RNA transcripts. The canonical MSI1 binding site (MBS), A/GU(1-3)AG single-strand motif, is present in many RNA virus genomes, but only Zika virus (ZIKV) genome has been demonstrated to bind MSI1. Herein, we identified the AUAG motif and the AGAA tetraloop in the Xrn1-resistant RNA 2 (xrRNA2) as the canonical and non-canonical MBS, respectively, and both are crucial for ZIKV neurotropism. More importantly, the unique AGNN-type tetraloop is evolutionally conserved, and distinguishes ZIKV from other known viruses with putative MBSs. Integrated structural analysis showed that MSI1 binds to the AUAG motif and AGAA tetraloop of ZIKV in a bipartite fashion. Thus, our results not only identified an unusual viral RNA structure responsible for MSI recognition, but also revealed a role for the highly structured xrRNA in controlling viral neurotropism.
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Affiliation(s)
- Xiang Chen
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Yan Wang
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhonghe Xu
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng-Li Cheng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Qing-Qing Ma
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Rui-Ting Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Zheng-Jian Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Hui Zhao
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China.
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13
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Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T. Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 2023; 14:772. [PMID: 36774373 PMCID: PMC9922296 DOI: 10.1038/s41467-023-36402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
The S. pombe orthologue of the human PAXT connection, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex that targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identify and characterise the interaction between Pla1 and the MTREC complex core component Red1 and analyse the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex shows that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations show that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction is also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3'-end processing machineries.
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Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Anusree Sivadas
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Nikolay Dobrev
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Rippei Hayashi
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Leo Kiss
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Meyerhofstr, 1, D-69117, Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany.
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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14
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Korn SM, Von Ehr J, Dhamotharan K, Tants JN, Abele R, Schlundt A. Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein. Int J Mol Sci 2023; 24:ijms24043286. [PMID: 36834708 PMCID: PMC9958909 DOI: 10.3390/ijms24043286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately 100 kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA and RNA binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerize, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
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Affiliation(s)
- Sophie M. Korn
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Julian Von Ehr
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- Correspondence:
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15
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Liu Y, Abula A, Xiao H, Guo H, Li T, Zheng L, Chen B, Nguyen HC, Ji X. Structural Insight Into hnRNP A2/B1 Homodimerization and DNA Recognition. J Mol Biol 2023; 435:167920. [PMID: 36528084 DOI: 10.1016/j.jmb.2022.167920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) has been identified as a nuclear DNA sensor. Upon viral infection, hnRNP A2/B1 recognizes pathogen-derived DNA as a homodimer, which is a prerequisite for its translocation to the cytoplasm to activate the interferon response. However, the DNA binding mechanism inducing hnRNP A2/B1 homodimerization is unknown. Here, we show the crystal structure of the RNA recognition motif (RRM) of hnRNP A2/B1 in complex with a U-shaped ssDNA, which mediates the formation of a newly observed protein dimer. Our biochemical assays and mutagenesis studies confirm that the hnRNP A2/B1 homodimer forms in solution by binding to pre-generated ssDNA or dsDNA with a U-shaped bulge. These results depict a potential functional state of hnRNP A2/B1 in antiviral immunity and other cellular processes.
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Affiliation(s)
- Yue Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Abudureyimu Abula
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China; School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830054, People's Republic of China
| | - Haonan Xiao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Tinghan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Biqing Chen
- Research Center of Chinese Medicine/Central Laboratory, Jiangsu Province Hospital of Chinese Medicine/ the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, People's Republic of China
| | - Henry C Nguyen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, People's Republic of China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, People's Republic of China.
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16
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Agarwal A, Bahadur RP. Modular architecture and functional annotation of human RNA-binding proteins containing RNA recognition motif. Biochimie 2023; 209:116-130. [PMID: 36716848 DOI: 10.1016/j.biochi.2023.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/09/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
RNA-binding proteins (RBPs) are structurally and functionally diverse macromolecules with significant involvement in several post-transcriptional gene regulatory processes and human diseases. RNA recognition motif (RRM) is one of the most abundant RNA-binding domains in human RBPs. The unique modular architecture of each RBP containing RRM is crucial for its diverse target recognition and function. Genome-wide study of these structurally conserved and functionally diverse domains can enhance our understanding of their functional implications. In this study, modular architecture of RRM containing RBPs in human proteome is identified and systematically analysed. We observe that 30% of human RBPs with RNA-binding function contain RRM in single or multiple repeats or with other domains with maximum of six repeats. Zinc-fingers are the most frequently co-occurring domain partner of RRMs. Human RRM containing RBPs mostly belong to RNA metabolism class of proteins and are significantly enriched in two functional pathways including spliceosome and mRNA surveillance. Various human diseases are associated with 18% of the RRM containing RBPs. Single RRM containing RBPs are highly enriched in disorder regions. Gene ontology (GO) molecular functions including poly(A), poly(U) and miRNA binding are highly depleted in RBPs with single RRM, indicating the significance of modular nature of RRMs in specific function. The current study reports all the possible domain architectures of RRM containing human RBPs and their functional enrichment. The idea of domain architecture, and how they confer specificity and new functionalities to RBPs, can help in re-designing of modular RRM containing RBPs with re-engineered function.
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Affiliation(s)
- Ankita Agarwal
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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17
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Papanikolaou NA, Nikolaidis M, Amoutzias GD, Fouza A, Papaioannou M, Pandey A, Papavassiliou AG. The Dynamic and Crucial Role of the Arginine Methylproteome in Myoblast Cell Differentiation. Int J Mol Sci 2023; 24:2124. [PMID: 36768448 PMCID: PMC9916730 DOI: 10.3390/ijms24032124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
Protein arginine methylation is an extensive and functionally significant post-translational modification. However, little is known about its role in differentiation at the systems level. Using stable isotope labeling by amino acids in cell culture (SILAC) proteomics of whole proteome analysis in proliferating or five-day differentiated mouse C2C12 myoblasts, followed by high-resolution mass spectrometry, biochemical assays, and specific immunoprecipitation of mono- or dimethylated arginine peptides, we identified several protein families that were differentially methylated on arginine. Our study is the first to reveal global changes in the arginine mono- or dimethylation of proteins in proliferating myoblasts and differentiated myocytes and to identify enriched protein domains and novel short linear motifs (SLiMs). Our data may be crucial for dissecting the links between differentiation and cancer growth.
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Affiliation(s)
- Nikolaos A. Papanikolaou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larisa, Greece
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larisa, Greece
| | - Ariadni Fouza
- Fifth Surgical Department, Ippokrateio General Hospital, School of Medicine, Aristotle University of Thessaloniki, 54643 Thessaloniki, Macedonia, Greece
| | - Maria Papaioannou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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18
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523326. [PMID: 36711508 PMCID: PMC9882015 DOI: 10.1101/2023.01.09.523326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | | | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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Sobeh AM, Eichhorn CD. C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition. Biophys Chem 2023; 292:106928. [PMID: 36427363 PMCID: PMC9768861 DOI: 10.1016/j.bpc.2022.106928] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7) containing an RNA recognition motif (RRM) was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we found that RRM constructs containing extended C-termini have increased solubility compared to a minimal RRM construct, although these constructs aggregate in a temperature and concentration-dependent manner. Using solution NMR dynamics experiments, we identified additional structural features observed previously in crystal but not in solution structures. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 primarily crosslinks to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.
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Affiliation(s)
- Amr M Sobeh
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA
| | - Catherine D Eichhorn
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA.
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20
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Krepl M, Pokorná P, Mlýnský V, Stadlbauer P, Šponer J. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Res 2022; 50:12480-12496. [PMID: 36454011 PMCID: PMC9757038 DOI: 10.1093/nar/gkac1106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.
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Affiliation(s)
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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21
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Jing Z, Ren P. Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model. J Phys Chem B 2022; 126:7343-7353. [PMID: 36107618 PMCID: PMC9530969 DOI: 10.1021/acs.jpcb.2c05278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-RNA interactions are integral to the biological functions of RNA. It is well recognized that molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than those of each component. The difficulty arises from the strong electrostatic interactions and the delicate balance between various types of physical forces at the interface. Previously, MD simulations of protein-RNA complexes have predominantly employed fixed-charge force fields. Although force field modifications have been developed to address problems identified in the simulations, some protein-RNA structures are still hard to reproduce by simulations. Here, we present MD simulations of two representative protein-RNA complexes using the AMOEBA polarizable force field. The van der Waals parameters were refined to reproduce accurate quantum-mechanical data of base-base and base-amino acid interactions. It was found that the refined parameters produced a more stable hydrogen-bond network in the interface. One of the complexes remained stable during the short simulations, whereas it could quickly break down in previous simulations using fixed-charge force fields. There was reversible breaking and formation of hydrogen bonds that are observed in the crystal structure, which may indicate the difference in solution and crystal structures. While further improvement and validation of the force fields are still needed, this work demonstrates that polarizable force fields are promising for the study of protein-RNA complexes.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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22
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Li J, Fang P, Zhou Y, Wang D, Fang L, Xiao S. DEAD-box RNA helicase 21 negatively regulates cytosolic RNA-mediated innate immune signaling. Front Immunol 2022; 13:956794. [PMID: 36032158 PMCID: PMC9399600 DOI: 10.3389/fimmu.2022.956794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
DEAD-box RNA helicase 21 (DDX21), also known as RHII/Gu, is an ATP-dependent RNA helicase. In addition to playing a vital role in regulating cellular RNA splicing, transcription, and translation, accumulated evidence has suggested that DDX21 is also involved in the regulation of innate immunity. However, whether DDX21 induces or antagonizes type I interferon (IFN-I) production has not been clear and most studies have been performed through ectopic overexpression or RNA interference-mediated knockdown. In this study, we generated DDX21 knockout cell lines and found that knockout of DDX21 enhanced Sendai virus (SeV)-induced IFN-β production and IFN-stimulated gene (ISG) expression, suggesting that DDX21 is a negative regulator of IFN-β. Mechanistically, DDX21 competes with retinoic acid-inducible gene I (RIG-I) for binding to double-stranded RNA (dsRNA), thereby attenuating RIG-I-mediated IFN-β production. We also identified that the 217-784 amino acid region of DDX21 is essential for binding dsRNA and associated with its ability to antagonize IFN production. Taken together, our results clearly demonstrated that DDX21 negatively regulates IFN-β production and functions to maintain immune homeostasis.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yanrong Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China,*Correspondence: Shaobo Xiao,
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23
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Xu W, Dou Y, Geng H, Fu J, Dan Z, Liang T, Cheng M, Zhao W, Zeng Y, Hu Z, Huang W. OsGRP3 Enhances Drought Resistance by Altering Phenylpropanoid Biosynthesis Pathway in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23137045. [PMID: 35806050 PMCID: PMC9266740 DOI: 10.3390/ijms23137045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation.
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Affiliation(s)
- Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangfan Dou
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jinmei Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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24
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Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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25
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Sun A, Li Y, He Y, Zou X, Chen F, Ji R, You C, Yu K, Li Y, Xiao W, Guo X. Comprehensive Genome-Wide Identification, Characterization, and Expression Analysis of CCHC-Type Zinc Finger Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:892105. [PMID: 35574096 PMCID: PMC9100697 DOI: 10.3389/fpls.2022.892105] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The CCHC-type zinc finger proteins (CCHC-ZFPs) play versatile roles in plant growth, development and adaptation to the environment. However, little is known about functions of CCHC-ZFP gene family memebers in Triticum aestivum. In the present study, we identified a total of 50 TaCCHC-ZFP genes from the 21 wheat chromosomes, which were phylogenetically classified into eight groups based on their specific motifs and gene structures. The 43 segmentally duplicated TaCCHC-ZFP genes were retrieved, which formed 36 segmental duplication gene pairs. The collinearity analyses among wheat and other eight mono/dicots revealed that no gene pairs were found between wheat and the three dicots. The promoter analyses of the TaCCHC-ZFP genes showed that 636 environmental stress-responsive and phytohormone-responsive cis-elements. The gene ontology enrichment analysis indicated that all the TaCCHC-ZFP genes were annotated under nucleic acid binding and metal ion binding. A total of 91 MicroRNA (miRNA) binding sites were identified in 34 TaCCHC-ZFP genes according to the miRNA target analysis. Based on the public transcriptome data, the 38 TaCCHC-ZFP genes were identified as differentially expressed gene. The expression profiles of 15 TaCCHC-ZFP genes were verified by the quantitative real-time PCR assays, and the results showed that these genes were responsive to drought or heat treatments. Our work systematically investigated the gene structures, evolutionary features, and potential functions of TaCCHC-ZFP genes. It lays a foundation for further research and application of TaCCHC-ZFP genes in genetic improvement of T. aestivum.
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26
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Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022; 30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.
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Affiliation(s)
- Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland; Systems Biology PhD Program, University of Zürich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland.
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27
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Zhang Y, Wu D, Wang Y, Xu X. Two types of C-terminal regions of RNA-binding proteins play distinct roles in stress tolerance of Synechocystis sp. PCC 6803. FEMS Microbiol Lett 2022; 369:6536912. [PMID: 35212739 PMCID: PMC9333190 DOI: 10.1093/femsle/fnac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/22/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
In the phylogenetic tree of RRM-type Rbps (RNA-binding proteins) in cyanobacteria, Rbp1 of Synechocystis 6803, with a single RRM (RNA recognition motif) region and a C-terminal glycine-rich region, and Rbp2, without the C-terminal region, both belong to the cluster I, whereas Rbp3 with a different type of C-terminal region is in the cluster II. Rbp1 is required for the cold adaptability of the cyanobacterium, and Rbp3 is for salt tolerance. Here, we report that the C-terminal region of Rbp1 is not required for the cold adaptability function but the C-terminal region of Rbp3 can direct the RRM of Rbp1 to the salt tolerance function. Bioinformatic and experimental analyses indicate that Rbps in cyanobacteria should be classified as two types. It is the first report for the distinct roles of C-terminal regions of Rbps in stress tolerance of cyanobacteria.
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Affiliation(s)
- Yueming Zhang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongqing Wu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yali Wang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xudong Xu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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28
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Soubise B, Jiang Y, Douet-Guilbert N, Troadec MB. RBM22, a Key Player of Pre-mRNA Splicing and Gene Expression Regulation, Is Altered in Cancer. Cancers (Basel) 2022; 14:cancers14030643. [PMID: 35158909 PMCID: PMC8833553 DOI: 10.3390/cancers14030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/05/2023] Open
Abstract
RNA-Binding Proteins (RBP) are very diverse and cover a large number of functions in the cells. This review focuses on RBM22, a gene encoding an RBP and belonging to the RNA-Binding Motif (RBM) family of genes. RBM22 presents a Zinc Finger like and a Zinc Finger domain, an RNA-Recognition Motif (RRM), and a Proline-Rich domain with a general structure suggesting a fusion of two yeast genes during evolution: Cwc2 and Ecm2. RBM22 is mainly involved in pre-mRNA splicing, playing the essential role of maintaining the conformation of the catalytic core of the spliceosome and acting as a bridge between the catalytic core and other essential protein components of the spliceosome. RBM22 is also involved in gene regulation, and is able to bind DNA, acting as a bona fide transcription factor on a large number of target genes. Undoubtedly due to its wide scope in the regulation of gene expression, RBM22 has been associated with several pathologies and, notably, with the aggressiveness of cancer cells and with the phenotype of a myelodysplastic syndrome. Mutations, enforced expression level, and haploinsufficiency of RBM22 gene are observed in those diseases. RBM22 could represent a potential therapeutic target in specific diseases, and, notably, in cancer.
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Affiliation(s)
- Benoît Soubise
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
| | - Yan Jiang
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- Department of Hematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Nathalie Douet-Guilbert
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
| | - Marie-Bérengère Troadec
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
- Correspondence: ; Tel.: +33-2-98-01-64-55
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29
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Jonely M, Singh RK, Donelick HM, Bass BL, Noriega R. Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA. Chem Commun (Camb) 2021; 57:10879-10882. [PMID: 34590626 DOI: 10.1039/d1cc03843e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dicer-2 cleaves double-stranded RNA into siRNAs in a terminus-dependent manner as part of D. melanogaster's RNA interference pathway. Using ultrafast fluorescence, we probe the local environment of chromophores at the dsRNA terminus upon binding by Dicer-2 and interrogate the effects of Loquacious-PD, an accessory protein. We find substrate-selective modes of molecular recognition that distinguish between blunt and 3'overhang termini, but whose differences are greatly reduced by Loquacious-PD. These results connect the molecular recognition properties of Dicer-2 to its selective processing of dsRNAs with different termini and to its need for Loquacious-PD to efficiently produce endogenous siRNAs.
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Affiliation(s)
- McKenzie Jonely
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
| | - Raushan K Singh
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Helen M Donelick
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Brenda L Bass
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Rodrigo Noriega
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
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30
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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31
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Aggarwal P, Bhavesh NS. Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter. Nucleic Acids Res 2021; 49:5943-5955. [PMID: 33999211 PMCID: PMC8191779 DOI: 10.1093/nar/gkab363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/02/2021] [Accepted: 04/24/2021] [Indexed: 01/07/2023] Open
Abstract
DNA binding proteins recognize DNA specifically or non-specifically using direct and indirect readout mechanisms like sliding, hopping, and diffusion. However, a common difficulty in explicitly elucidating any particular mechanism of site-specific DNA-protein recognition is the lack of knowledge regarding target sequences and inadequate account of non-specific interactions, in general. Here, we decipher the structural basis of target search performed by the key regulator of expression of c-myc proto-oncogene, the human RBMS1 protein. In this study, we have shown the structural reorganization of this multi-domain protein required for recognizing the specific c-myc promoter sequence. The results suggest that a synergy between structural re-organization and thermodynamics is necessary for the recognition of target sequences. The study presents another perspective of looking at the DNA-protein interactions.
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Affiliation(s)
- Priyanka Aggarwal
- Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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32
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Zhou Q, Usluer S, Zhang F, Lenard AJ, Bourgeois BMR, Madl T. ATP regulates RNA-driven cold inducible RNA binding protein phase separation. Protein Sci 2021; 30:1438-1453. [PMID: 33991007 PMCID: PMC8197425 DOI: 10.1002/pro.4123] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 01/12/2023]
Abstract
Intrinsically disordered proteins and proteins containing intrinsically disordered regions are highly abundant in the proteome of eukaryotes and are extensively involved in essential biological functions. More recently, their role in the organization of biomolecular condensates has become evident and along with their misregulation in several neurologic disorders. Currently, most studies involving these proteins are carried out in vitro and using purified proteins. Given that in cells, condensate‐forming proteins are exposed to high, millimolar concentrations of cellular metabolites, we aimed to reveal the interactions of cellular metabolites and a representative condensate‐forming protein. Here, using the arginine–glycine/arginine–glycine–glycine (RG/RGG)‐rich cold inducible RNA binding protein (CIRBP) as paradigm, we studied binding of the cellular metabolome to CIRBP. We found that most of the highly abundant cellular metabolites, except nucleotides, do not directly bind to CIRBP. ATP, ADP, and AMP as well as NAD+, NADH, NADP+, and NADPH directly interact with CIRBP, involving both the folded RNA‐recognition motif and the disordered RG/RGG region. ATP binding inhibited RNA‐driven phase separation of CIRBP. Thus, it might be beneficial to include cellular metabolites in in vitro liquid–liquid phase separation studies of RG/RGG and other condensate‐forming proteins in order to better mimic the cellular environment in the future.
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Affiliation(s)
- Qishun Zhou
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria
| | - Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin M R Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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33
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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34
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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35
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Marcaida MJ, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe MC, Adebajo D, Manley S, Trono D, Dal Peraro M. The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity. iScience 2020; 23:101811. [PMID: 33313488 PMCID: PMC7721647 DOI: 10.1016/j.isci.2020.101811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological functions is not well understood. In this work, we show that DDX21, a human DEAD-box helicase with RNA G-quadruplex resolving activity, is dimeric and that its oligomerization state influences its helicase activity. Solution small-angle X-ray scattering (SAXS) analysis uncovers a flexible multi-domain protein with a central dimerization domain. While the Arg/Gly rich C termini, rather than dimerization, are key to maintaining high affinity for RNA substrates, in vitro helicase assays indicate that an intact dimer is essential for both DDX21 ATP-dependent double-stranded RNA unwinding and ATP-independent G-quadruplex remodeling activities. Our results suggest that oligomerization plays a key role in regulating RNA DEAD-box helicase activity. The human RNA DEAD-box helicase DDX21 is dimeric DDX21 dimerization is mediated by a hydrophobic central core domain SAXS-based modeling reveals that DDX21 is intrinsically flexible Dimerization and C-terminal domains mediate G-quadruplex and dsRNA unwinding
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Affiliation(s)
- Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Annamaria Kauzlaric
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Alice Duperrex
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Jenny Sülzle
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Martin C Moncrieffe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Damilola Adebajo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
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36
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Upadhyay SK, Mackereth CD. Structural basis of UCUU RNA motif recognition by splicing factor RBM20. Nucleic Acids Res 2020; 48:4538-4550. [PMID: 32187365 PMCID: PMC7192616 DOI: 10.1093/nar/gkaa168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
The vertebrate splicing factor RBM20 (RNA binding motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four nucleotide RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.
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Affiliation(s)
| | - Cameron D Mackereth
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France.,Inserm U1212, CNRS UMR5320, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
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37
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Maris C, Jayne S, Damberger FF, Beusch I, Dorn G, Ravindranathan S, Allain FHT. A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure. Nucleic Acids Res 2020; 48:4521-4537. [PMID: 32170319 PMCID: PMC7192611 DOI: 10.1093/nar/gkaa155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alternative splicing, mRNA localization, stabilization, polyadenylation and translation initiation from internal ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5′-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA recognition motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.
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Affiliation(s)
| | - Sandrine Jayne
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | | | - Irene Beusch
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
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38
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Structural basis for mRNA recognition by human RBM38. Biochem J 2020; 477:161-172. [PMID: 31860021 DOI: 10.1042/bcj20190652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/29/2022]
Abstract
RNA-binding protein RBM38 was reported to bind the mRNA of several p53-related genes through its RRM domain and to up-regulate or down-regulate protein translation by increasing mRNA stability or recruitment of other effector proteins. The recognition mechanism, however, for RNA-binding of RBM38 remains unclear. Here, we report the crystal structure of the RRM domain of human RBM38 in complex with a single-stranded RNA. Our structural and biological results revealed that RBM38 recognizes G(U/C/A)GUG sequence single-stranded RNA in a sequence-specific and structure-specific manner. Two phenylalanine stacked with bases of RNA were crucial for RNA binding, and a series of hydrogen bonds between the base atoms of RNA and main-chain or side-chain atoms of RBM38 determine the sequence-specific recognition. Our results revealed the RNA-recognition mechanism of human RBM38 and provided structural information for understanding the RNA-binding property of RBM38.
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39
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Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5. J Mol Biol 2020; 432:4127-4138. [PMID: 32450081 DOI: 10.1016/j.jmb.2020.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/22/2022]
Abstract
The multi-domain RNA binding protein RBM5 is a molecular signature of metastasis. RBM5 regulates alternative splicing of apoptotic genes including the cell death receptor Fas and the initiator Caspase-2. The RBM5 RanBP2-type zinc finger (Zf1) is known to specifically recognize single-stranded RNAs with high affinity. Here, we study the structure and conformational dynamics of the Zf1 zinc finger of human RBM5 using NMR. We show that the presence of a non-canonical cysteine in Zf1 kinetically destabilizes the protein. Metal-exchange kinetics show that mutation of the cysteine establishes high-affinity coordination of the zinc. Our data indicate that selection of such a structurally destabilizing mutation during the course of evolution could present an opportunity for functional adaptation of the protein.
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40
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Su WC, Harrison PM. Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives. PeerJ 2020; 8:e9023. [PMID: 32337108 PMCID: PMC7169965 DOI: 10.7717/peerj.9023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Pub1 protein is an important RNA-binding protein functional in stress granule assembly in budding yeast Saccharomyces cerevisiae and, as its co-ortholog Tia1, in humans. It is unique among proteins in evidencing prion-like aggregation in both its yeast and human forms. Previously, we noted that Pub1/Tia1 was the only protein linked to human disease that has prion-like character and and has demonstrated such aggregation in both species. Thus, we were motivated to probe further into the evolution of the Pub1/Tia1 family (and its close relative Nam8 and its orthologs) to gain a picture of how such a protein has evolved over deep evolutionary time since the last common ancestor of eukaryotes. Here, we discover that the prion-like composition of this protein family is deeply conserved across eukaryotes, as is the prion-like composition of its close relative Nam8/Ngr1. A sizeable minority of protein orthologs have multiple prion-like domains within their sequences (6-20% depending on criteria). The number of RNA-binding RRM domains is conserved at three copies over >86% of the Pub1 family (>71% of the Nam8 family), but proteins with just one or two RRM domains occur frequently in some clades, indicating that these are not due to annotation errors. Overall, our results indicate that a basic scaffold comprising three RNA-binding domains and at least one prion-like region has been largely conserved since the last common ancestor of eukaryotes, providing further evidence that prion-like aggregation may be a very ancient and conserved phenomenon for certain specific proteins.
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Affiliation(s)
- Wan-Chun Su
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada
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41
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Williams FP, Haubrich K, Perez-Borrajero C, Hennig J. Emerging RNA-binding roles in the TRIM family of ubiquitin ligases. Biol Chem 2020; 400:1443-1464. [PMID: 31120853 DOI: 10.1515/hsz-2019-0158] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
TRIM proteins constitute a large, diverse and ancient protein family which play a key role in processes including cellular differentiation, autophagy, apoptosis, DNA repair, and tumour suppression. Mostly known and studied through the lens of their ubiquitination activity as E3 ligases, it has recently emerged that many of these proteins are involved in direct RNA binding through their NHL or PRY/SPRY domains. We summarise the current knowledge concerning the mechanism of RNA binding by TRIM proteins and its biological role. We discuss how RNA-binding relates to their previously described functions such as E3 ubiquitin ligase activity, and we will consider the potential role of enrichment in membrane-less organelles.
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Affiliation(s)
- Felix Preston Williams
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kevin Haubrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Cecilia Perez-Borrajero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, e-mail:
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42
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Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins. Int J Mol Sci 2020; 21:ijms21072289. [PMID: 32225071 PMCID: PMC7177541 DOI: 10.3390/ijms21072289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208–218 and ~270–284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.
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43
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Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
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44
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Aznarez I, Nomakuchi TT, Tetenbaum-Novatt J, Rahman MA, Fregoso O, Rees H, Krainer AR. Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Rep 2019; 23:2186-2198. [PMID: 29768215 PMCID: PMC5999336 DOI: 10.1016/j.celrep.2018.04.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/20/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022] Open
Abstract
The splicing factor SRSF1 promotes nonsense-mediated mRNA decay (NMD), a quality control mechanism that degrades mRNAs with premature termination codons (PTCs). Here we show that transcript-bound SRSF1 increases the binding of NMD factor UPF1 to mRNAs while in, or associated with, the nucleus, bypassing UPF2 recruitment and promoting NMD. SRSF1 promotes NMD when positioned downstream of a PTC, which resembles the mode of action of exon junction complex (EJC) and NMD factors. Moreover, splicing and/or EJC deposition increase the effect of SRSF1 on NMD. Lastly, SRSF1 enhances NMD of PTC-containing endogenous transcripts that result from various events. Our findings reveal an alternative mechanism for UPF1 recruitment, uncovering an additional connection between splicing and NMD. SRSF1’s role in the mRNA’s journey from splicing to decay has broad implications for gene expression regulation and genetic diseases.
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Affiliation(s)
- Isabel Aznarez
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | | - Oliver Fregoso
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Holly Rees
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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45
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Travis B, Shaw PLR, Liu B, Ravindra K, Iliff H, Al-Hashimi HM, Schumacher MA. The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA. Nucleic Acids Res 2019; 47:2130-2142. [PMID: 30544166 PMCID: PMC6393287 DOI: 10.1093/nar/gky1259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
Kinetoplastid RNA (kRNA) editing takes place in the mitochondria of kinetoplastid protists and creates translatable mRNAs by uridine insertion/deletion. Extensively edited (pan-edited) transcripts contain quadruplex forming guanine stretches, which must be remodeled to promote uridine insertion/deletion. Here we show that the RRM domain of the essential kRNA-editing factor TbRGG2 binds poly(G) and poly(U) RNA and can unfold both. A region C-terminal to the RRM mediates TbRGG2 dimerization, enhancing RNA binding. A RRM-U4 RNA structure reveals a unique RNA-binding mechanism in which the two RRMs of the dimer employ aromatic residues outside the canonical RRM RNA-binding motifs to encase and wrench open the RNA, while backbone atoms specify the uridine bases. Notably, poly(G) RNA is bound via a different binding surface. Thus, these data indicate that TbRGG2 RRM can bind and remodel several RNA substrates suggesting how it might play multiple roles in the kRNA editing process.
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Affiliation(s)
- Brady Travis
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Porsha L R Shaw
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Krishna Ravindra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hadley Iliff
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Chemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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46
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:11/7/a032359. [PMID: 31262947 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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47
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Domingo J, Baeza-Centurion P, Lehner B. The Causes and Consequences of Genetic Interactions (Epistasis). Annu Rev Genomics Hum Genet 2019; 20:433-460. [PMID: 31082279 DOI: 10.1146/annurev-genom-083118-014857] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.
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Affiliation(s)
- Júlia Domingo
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , , .,Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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48
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Meyer A, Golbik RP, Sänger L, Schmidt T, Behrens SE, Friedrich S. The RGG/RG motif of AUF1 isoform p45 is a key modulator of the protein's RNA chaperone and RNA annealing activities. RNA Biol 2019; 16:960-971. [PMID: 30951406 DOI: 10.1080/15476286.2019.1602438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The RNA-binding protein AUF1 regulates post-transcriptional gene expression by affecting the steady state and translation levels of numerous target RNAs. Remodeling of RNA structures by the largest isoform AUF1 p45 was recently demonstrated in the context of replicating RNA viruses, and involves two RNA remodeling activities, i.e. an RNA chaperone and an RNA annealing activity. AUF1 contains two non-identical RNA recognition motifs (RRM) and one RGG/RG motif located in the C-terminus. In order to determine the functional significance of each motif to AUF1's RNA-binding and remodeling activities we performed a comprehensive mutagenesis study and characterized the wildtype AUF1, and several variants thereof. We demonstrate that each motif contributes to efficient RNA binding and remodeling by AUF1 indicating a tight cooperation of the RRMs and the RGG/RG motif. Interestingly, the data identify two distinct roles for the arginine residues of the RGG/RG motif for each RNA remodeling activity. First, arginine-mediated stacking interactions promote AUF1's helix-destabilizing RNA chaperone activity. Second, the electropositive character of the arginine residues is the major driving force for the RNA annealing activity. Thus, we provide the first evidence that arginine residues of an RGG/RG motif contribute to the mechanism of RNA annealing and RNA chaperoning.
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Affiliation(s)
- Alexandra Meyer
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Ralph P Golbik
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Lennart Sänger
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Tobias Schmidt
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Sven-Erik Behrens
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Susann Friedrich
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
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49
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Mohanty B, Hanson-Manful P, Finn TJ, Chambers CR, McKellar JLO, Macindoe I, Helder S, Setiyaputra S, Zhong Y, Mackay JP, Patrick WM. The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G. Proteins 2019; 87:699-705. [PMID: 30958578 DOI: 10.1002/prot.25687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/23/2019] [Accepted: 04/04/2019] [Indexed: 11/08/2022]
Abstract
InterPro family IPR020489 comprises ~1000 uncharacterized bacterial proteins. Previously we showed that overexpressing the Escherichia coli representative of this family, EcYejG, conferred low-level resistance to aminoglycoside antibiotics. In an attempt to shed light on the biochemical function of EcYejG, we have solved its structure using multinuclear solution NMR spectroscopy. The structure most closely resembles that of domain III from elongation factor G (EF-G). EF-G catalyzes ribosomal translocation and mutations in EF-G have also been associated with aminoglycoside resistance. While we were unable to demonstrate a direct interaction between EcYejG and the ribosome, the protein might play a role in translation.
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Affiliation(s)
- Biswaranjan Mohanty
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Paulina Hanson-Manful
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | | | - Ingrid Macindoe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Helder
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Surya Setiyaputra
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University, Wellington, New Zealand
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50
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Lenka SK, Singh AK, Muthusamy SK, Smita S, Chinnusamy V, Bansal KC. Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:482-491. [PMID: 30940336 DOI: 10.1071/fp18241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
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Affiliation(s)
- Sangram K Lenka
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India
| | - Amit K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Senthilkumar K Muthusamy
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India
| | - Shuchi Smita
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Viswanathan Chinnusamy
- ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India
| | - Kailash C Bansal
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author.
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